chrX-152487090-T-C

Variant names:

• chrX-152487090-T-C
• rs10856240

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.63 (16982 hom., 20349 hem., cov: 23)
  • Failed GnomAD Quality Control
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109
• Publications: 1 publications found

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.626 AC: 69066 AN: 110244 Hom.: 16993 Cov.: 23

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.956

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.416

Gnomad SAS AF: 0.615

Gnomad FIN AF: 0.851

Gnomad MID AF: 0.734

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.638

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.626 AC: 69056 AN: 110293 Hom.: 16982 Cov.: 23 AF XY: 0.625 AC XY: 20349 AN XY: 32579

African (AFR) AF: 0.328 AC: 10003 AN: 30453

American (AMR) AF: 0.565 AC: 5838 AN: 10341

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 1783 AN: 2635

East Asian (EAS) AF: 0.416 AC: 1439 AN: 3455

South Asian (SAS) AF: 0.616 AC: 1622 AN: 2631

European-Finnish (FIN) AF: 0.851 AC: 4870 AN: 5721

Middle Eastern (MID) AF: 0.726 AC: 151 AN: 208

European-Non Finnish (NFE) AF: 0.793 AC: 41760 AN: 52674

Other (OTH) AF: 0.629 AC: 940 AN: 1495

Alfa AF: 0.649 Hom.: 29159

Bravo AF: 0.594

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.63
PhyloP100		-0.11

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10856240; hg19: chrX-151655562;